library(dplyr)
library(Hmisc)
library(rms)
library(summarytools)
library(consort)
library(gtsummary)
library(gt)
library(ggplot2)
library(glue)
library(htmlwidgets)

This .Rmd file was written with the aim to aid you when writing your first reports in R Markdown. It contains the most important features for creating a good reproducible report. The structure followed is not necessarily the one you should follow when performing your data analysis or reporting your results. The purpose of this template is simply to present you with a good structure for the data report and the code behind it.

The structure used in this R Markdown report is the following:

Background - describe in a concise way the background of the research field, the research question of interest, etc
Data dictionary - makes it easier for the reader to know the meaning of each variable. Can select those variables of interest for analysis, no need to show the whole data set
Flowchart - Show how many patients are excluded from the analysis
Descriptive statistics - show univariable analysis for continuous and categorical variables so the audience has a good overlook of the data.
Table 1 - There are better ways of describing your data, but everybody wants to see a Table 1
Model - Visualize your model and your effects
Conclusion
Computer environment - always include the computer environment used. It fosters reproducibility
Update history - optional. To show changes over time in your report.

Through this report I have used different chunk options. Below a short summary of the ones I have used. For a detail explanation of these and many other chunk options, please check this.

echo = FALSE hide code (default is TRUE hence code is displayed) but result is shown
warning = FALSE drop warnings from output document (default is TRUE)
message = FALSE suppress messages (default is TRUE)
eval = FALSE do not evaluate the code (default is TRUE) but the code appears if echo=T was chosen
include = FALSE to hide both the code and the result from the rendered document but the code is still evaluated
fig.align = to align the figure. Four options exist default, left, right or center
fig.cap = write a figure caption
fig.dim = c(7,8) choose dimensions of plot. Is a shorthand of fig.width = 7, fig.height = 8.
out.width = 70% and out.height = 80% width and height of the plot in the output document, which can be different with its physical fig.width and fig.height, i.e., plots can be scaled in the output document.
dpi = dots per inch value (for image resolution). Default is 72

Note that this .Rmd file was written with the intention to knit to HTML. I believe that HTML files have more advantages than pdf or word files and are easier to present to your PI or colleagues.

How to insert references in your Report?

I personally prefer to use hyperlinks than references because it allows users to access the specific manuscript or book directly. However, a reference Section at the end of your Report might be of interest to have a quick overview of the bibliography used.

To do this you will need to create a plain-text file with the .bib extension that consists of bibliography entries. You can do this automatically with the knitr::write_bib() function. This function uses utils::citation() and utils::toBibtex() to create bib entries for R packages and write them in a file.

# automatically create a bib database for R packages 
knitr::write_bib(x = c('knitr', 'rmarkdown'), #specify package name(s).
                 file = 'packages.bib') # the .bib file to write

You can also use the .packages() argument. This will create a bib entry for all R packages loaded in the report, on top of the packages you specified manually.

knitr::write_bib(x = c(.packages(), 'knitr', 'rmarkdown'), # .packages() will create a bib entry for all R packages used in the report
                 file = 'packages.bib') # the .bib file to write

Items can be cited directly within the documentation using the syntax @key where key is the citation key in the first line of the entry. For example:

The main packages needed to create an R Markdown report are the rmarkdown package (Allaire et al. 2022) and the knitr package (Xie 2022). To read more about the rmarkdown package, read the R Markdown: the definitive guide book (Xie, Allaire, and Grolemund 2018) or the R Markdown Cookbook (Xie, Dervieux, and Riederer 2020).

The references will be automatically created at the end of your R Markdown report file. Importantly, to insert references in your R Markdown report you will need to specify a bibliography file using the bibliography metadata field in YAML.

You can also create a .bib file manually and insert references by hand. Simply use the utils::citation() function to see how to cite R and R packages.

citation(package = "base")

## 
## To cite R in publications use:
## 
##   R Core Team (2021). R: A language and environment for statistical
##   computing. R Foundation for Statistical Computing, Vienna, Austria.
##   URL https://www.R-project.org/.
## 
## A BibTeX entry for LaTeX users is
## 
##   @Manual{,
##     title = {R: A Language and Environment for Statistical Computing},
##     author = {{R Core Team}},
##     organization = {R Foundation for Statistical Computing},
##     address = {Vienna, Austria},
##     year = {2021},
##     url = {https://www.R-project.org/},
##   }
## 
## We have invested a lot of time and effort in creating R, please cite it
## when using it for data analysis. See also 'citation("pkgname")' for
## citing R packages.

You would copy the output BibTeX entry into your .bib file.

Background

The Gusto-I trial was a randomized trial comparing 4 thrombolytic strategies for acute myocardial infarction. The original study can be found here.

knitr::include_graphics("./Figures/Gusto_NEJM.png") #need to download Figure from Repository (or simply suppress this chunk with eval=FALSE)

GUSTO-I trial published in the NEJM.

Our aim is to derive a model for predicting 30-day mortality. Because this is simply a template for showing how to use R Markdown, I will not go into much detail and will simply get to the stage of model derivation and showing partial effect plots. Model validation with a resampling technique (e.g. bootstrap internal validation) will not be shown. Important aspects like discrimination and calibration of the model, shrinkage of coefficients for protection of future overfitting or plotting decision curve analysis for assessing net benefit of the model will not be shown here. ¹

Data

Data is obtained from http://hbiostat.org/data courtesy of the Vanderbilt University Department of Biostatistics.

load(url('http://hbiostat.org/data/gusto.rda'))
df <- as.data.frame(gusto)

Data dictionary

Hmisc::html(Hmisc::contents(df), levelType = 'table')

Data frame:df

40830 observations and 29 variables, maximum # NAs:10320

Name	Labels	Units	Levels	Class	Storage	NAs
day30					integer	0
sho					integer	0
hig					integer	0
dia	Diabetes			integer	integer	0
hyp					integer	0
hrt					integer	0
ttr	Time to Relief of Chest Pain > 1h			integer	integer	0
sex	Sex		2		integer	0
Killip	Killip Class		4		integer	0
age					double	0
ste	Number of ECG Leads with ST Elevation			numeric	integer	0
pulse	Heart Rate	beats/min		integer	integer	0
sysbp	Systolic Blood Pressure	mmHg		integer	integer	0
ant					integer	0
miloc	MI Location		3		integer	0
height	Height	cm		numeric	double	0
weight	Weight	kg		numeric	double	0
pmi	Previous MI		2		integer	0
htn	History of Hypertension			integer	integer	0
smk	Smoking		3		integer	0
pan					integer	0
fam	Family History of MI			integer	integer	0
prevcvd					integer	0
prevcabg					integer	0
regl					integer	0
grpl					integer	0
grps					integer	0
tpa					integer	10320
tx	Tx in 3 groups		3		integer	0

Variable	Levels
sex	male
	female
Killip	I
	II
	III
	IV
miloc	Inferior
	Other
	Anterior
pmi	no
	yes
smk	never
	quit
	current
tx	SK+tPA
	SK
	tPA

Patient Flowchart

We want to keep patients who received either streptokinase (SK) or primary angioplasty (tPA).

# dpi (dots per inch) for bitmap devices (dpi * inches = pixels). Default is 72
docl <- list()
docl[['all']] <- nrow(df)
docl[['sk_tPA']] <- table(df$tx)[1]
df <- df %>% filter(tx %in% c('SK', 'tPA'))
df$tx <- droplevels(df$tx) #tx was a three level categorical variable. Drop unused level (SK+tPA)
docl[['analysis']] <- nrow(df)

txt1 <- glue::glue("Patients recruited in \n the GUSTO-I trial \n (n={docl$all})")
txt1_side <- glue::glue("Excluded (n={docl$sk_tPA}):\n\u2022 Received SK+tPA (n={docl$sk_tPA})")
txt2 <- glue::glue("Main analysis \n (n={docl$analysis})")

flowchart <- consort::add_box(txt = txt1) %>% 
  consort::add_side_box(txt = txt1_side, dist = 0.05) %>%   
  consort::add_box(txt = txt2, dist = 0.05) 

plot(flowchart)

Patient flowchart using the {consort} package.

Descriptive statistics

Summary using `summarytools`

print(summarytools::dfSummary(df, 
                              varnumbers = FALSE,
                              valid.col = FALSE,
                              labels.col = FALSE,
                              graph.magnif = 0.76,
                              headings = F), 
      max.tbl.height = 300,
      method = "render")

Variable

Stats / Values

Freqs (% of Valid)

Graph

Missing

day30 [integer]

Min : 0

Mean : 0.1

Max : 1

0	:	28382	(	93.0%	)
1	:	2128	(	7.0%	)

0 (0.0%)

sho [integer]

Min : 0

Mean : 0

Max : 1

0	:	29864	(	97.9%	)
1	:	646	(	2.1%	)

0 (0.0%)

hig [integer]

Min : 0

Mean : 0.5

Max : 1

0	:	15603	(	51.1%	)
1	:	14907	(	48.9%	)

0 (0.0%)

dia [labelled, integer]

Min : 0

Mean : 0.1

Max : 1

0	:	25967	(	85.1%	)
1	:	4543	(	14.9%	)

0 (0.0%)

hyp [integer]

Min : 0

Mean : 0.1

Max : 1

0	:	28004	(	91.8%	)
1	:	2506	(	8.2%	)

0 (0.0%)

hrt [integer]

Min : 0

Mean : 0.3

Max : 1

0	:	20551	(	67.4%	)
1	:	9959	(	32.6%	)

0 (0.0%)

ttr [labelled, integer]

Min : 0

Mean : 0.6

Max : 1

0	:	10687	(	35.0%	)
1	:	19823	(	65.0%	)

0 (0.0%)

sex [labelled, factor]

1. male

2. female

22795	(	74.7%	)
7715	(	25.3%	)

0 (0.0%)

Killip [labelled, factor]

1. I

2. II

3. III

4. IV

26007	(	85.2%	)
3857	(	12.6%	)
417	(	1.4%	)
229	(	0.8%	)

0 (0.0%)

age [numeric]

Mean (sd) : 60.9 (11.9)

min ≤ med ≤ max:

19 ≤ 61.6 ≤ 110

IQR (CV) : 17.7 (0.2)

5342 distinct values

0 (0.0%)

ste [labelled, integer]

Mean (sd) : 4.1 (1.9)

min ≤ med ≤ max:

0 ≤ 4 ≤ 11

IQR (CV) : 3 (0.5)

12 distinct values

0 (0.0%)

pulse [labelled, integer]

Mean (sd) : 75.4 (17.8)

min ≤ med ≤ max:

0 ≤ 73 ≤ 220

IQR (CV) : 24 (0.2)

157 distinct values

0 (0.0%)

sysbp [labelled, integer]

Mean (sd) : 129 (23.9)

min ≤ med ≤ max:

0 ≤ 129.5 ≤ 280

IQR (CV) : 32 (0.2)

196 distinct values

0 (0.0%)

ant [integer]

Min : 0

Mean : 0.4

Max : 1

0	:	18644	(	61.1%	)
1	:	11866	(	38.9%	)

0 (0.0%)

miloc [labelled, factor]

1. Inferior

2. Other

3. Anterior

17582	(	57.6%	)
1062	(	3.5%	)
11866	(	38.9%	)

0 (0.0%)

height [labelled, numeric]

Mean (sd) : 171 (9.4)

min ≤ med ≤ max:

140 ≤ 172 ≤ 212.5

IQR (CV) : 12.8 (0.1)

506 distinct values

0 (0.0%)

weight [labelled, numeric]

Mean (sd) : 79.4 (15.8)

min ≤ med ≤ max:

36.7 ≤ 78 ≤ 213

IQR (CV) : 18.5 (0.2)

644 distinct values

0 (0.0%)

pmi [labelled, factor]

1. no

2. yes

25452	(	83.4%	)
5058	(	16.6%	)

0 (0.0%)

htn [labelled, integer]

Min : 1

Mean : 1.4

Max : 2

1	:	18875	(	61.9%	)
2	:	11635	(	38.1%	)

0 (0.0%)

smk [labelled, factor]

1. never

2. quit

3. current

13089	(	42.9%	)
8371	(	27.4%	)
9050	(	29.7%	)

0 (0.0%)

pan [integer]

Min : 1

Mean : 1.4

Max : 2

1	:	19165	(	62.8%	)
2	:	11345	(	37.2%	)

0 (0.0%)

fam [labelled, integer]

Min : 1

Mean : 1.4

Max : 2

1	:	17531	(	57.5%	)
2	:	12979	(	42.5%	)

0 (0.0%)

prevcvd [integer]

Min : 1

Mean : 1

Max : 2

1	:	29885	(	98.0%	)
2	:	625	(	2.0%	)

0 (0.0%)

prevcabg [integer]

Min : 1

Mean : 1

Max : 2

1	:	29145	(	95.5%	)
2	:	1365	(	4.5%	)

0 (0.0%)

regl [integer]

Mean (sd) : 8.6 (4.5)

min ≤ med ≤ max:

1 ≤ 9 ≤ 16

IQR (CV) : 7 (0.5)

16 distinct values

0 (0.0%)

grpl [integer]

Mean (sd) : 25.3 (14)

min ≤ med ≤ max:

1 ≤ 26 ≤ 48

IQR (CV) : 24 (0.6)

48 distinct values

0 (0.0%)

grps [integer]

Mean (sd) : 61.6 (34.8)

min ≤ med ≤ max:

1 ≤ 62 ≤ 121

IQR (CV) : 59 (0.6)

121 distinct values

0 (0.0%)

tpa [integer]

Min : 0

Mean : 0.3

Max : 1

0	:	20162	(	66.1%	)
1	:	10348	(	33.9%	)

0 (0.0%)

tx [factor]

1. SK

2. tPA

20162	(	66.1%	)
10348	(	33.9%	)

0 (0.0%)

Generated by summarytools 1.0.1 (R version 4.1.2)
2022-12-05

Summary using `Hmisc`

d <- Hmisc::describe(df)
Hmisc::html(d) #use scroll = TRUE for scrolling the output table

df

29 Variables 30510 Observations

day30

n	missing	distinct	Info	Sum	Mean	Gmd
30510	0	2	0.195	2128	0.06975	0.1298

sho

n	missing	distinct	Info	Sum	Mean	Gmd
30510	0	2	0.062	646	0.02117	0.04145

hig

n	missing	distinct	Info	Sum	Mean	Gmd
30510	0	2	0.75	14907	0.4886	0.4998

dia: Diabetes

n	missing	distinct	Info	Sum	Mean	Gmd
30510	0	2	0.38	4543	0.1489	0.2535

hyp

n	missing	distinct	Info	Sum	Mean	Gmd
30510	0	2	0.226	2506	0.08214	0.1508

hrt

n	missing	distinct	Info	Sum	Mean	Gmd
30510	0	2	0.66	9959	0.3264	0.4398

ttr: Time to Relief of Chest Pain > 1h

n	missing	distinct	Info	Sum	Mean	Gmd
30510	0	2	0.683	19823	0.6497	0.4552

sex: Sex

n	missing	distinct
30510	0	2

 Value        male female
 Frequency   22795   7715
 Proportion  0.747  0.253

Killip: Killip Class

n	missing	distinct
30510	0	4

 Value          I    II   III    IV
 Frequency  26007  3857   417   229
 Proportion 0.852 0.126 0.014 0.008

age

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
30510	0	5342	1	60.91	13.58	40.92	44.73	52.11	61.58	69.84	76.19	79.42

lowest : 19.027 20.781 20.969 20.984 21.449 , highest: 91.938 92.328 96.547 108.000 110.000

ste: Number of ECG Leads with ST Elevation

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
30510	0	12	0.961	4.093	2.11	1	2	3	4	6	7	7

lowest : 0 1 2 3 4 , highest: 7 8 9 10 11

 Value          0     1     2     3     4     5     6     7     8     9    10    11
 Frequency    465  1309  3437  9493  4333  3823  3413  2902  1059   247    26     3
 Proportion 0.015 0.043 0.113 0.311 0.142 0.125 0.112 0.095 0.035 0.008 0.001 0.000

pulse: Heart Rate beats/min

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
30510	0	157	0.999	75.38	19.5	50	55	62	73	86	98	107

lowest : 0 1 6 9 20 , highest: 191 200 205 210 220

sysbp: Systolic Blood Pressure mmHg

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
30510	0	196	0.999	129	26.58	92.0	100.0	112.0	129.5	144.0	160.0	170.0

lowest : 0 36 40 43 46 , highest: 266 274 275 276 280

ant

n	missing	distinct	Info	Sum	Mean	Gmd
30510	0	2	0.713	11866	0.3889	0.4753

miloc: MI Location

n	missing	distinct
30510	0	3

 Value      Inferior    Other Anterior
 Frequency     17582     1062    11866
 Proportion    0.576    0.035    0.389

height: Height cm

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
30510	0	506	0.999	171	10.61	154.9	157.5	165.0	172.0	177.8	182.8	185.4

lowest : 140.0 140.8 140.9 141.0 141.3 , highest: 207.0 208.0 208.2 210.8 212.5

weight: Weight kg

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
30510	0	644	1	79.43	17.29	56.00	60.39	69.50	78.00	88.00	100.00	107.00

lowest : 36.7 37.0 38.0 38.5 38.6 , highest: 182.0 184.0 185.0 188.0 213.0

pmi: Previous MI

n	missing	distinct
30510	0	2

 Value         no   yes
 Frequency  25452  5058
 Proportion 0.834 0.166

htn: History of Hypertension

n	missing	distinct	Info	Mean	Gmd
30510	0	2	0.708	1.381	0.4719

 Value          1     2
 Frequency  18875 11635
 Proportion 0.619 0.381

smk: Smoking

n	missing	distinct
30510	0	3

 Value        never    quit current
 Frequency    13089    8371    9050
 Proportion   0.429   0.274   0.297

pan

n	missing	distinct	Info	Mean	Gmd
30510	0	2	0.701	1.372	0.4672

 Value          1     2
 Frequency  19165 11345
 Proportion 0.628 0.372

fam: Family History of MI

n	missing	distinct	Info	Mean	Gmd
30510	0	2	0.733	1.425	0.4889

 Value          1     2
 Frequency  17531 12979
 Proportion 0.575 0.425

prevcvd

n	missing	distinct	Info	Mean	Gmd
30510	0	2	0.06	1.02	0.04013

 Value          1     2
 Frequency  29885   625
 Proportion  0.98  0.02

prevcabg

n	missing	distinct	Info	Mean	Gmd
30510	0	2	0.128	1.045	0.08548

 Value          1     2
 Frequency  29145  1365
 Proportion 0.955 0.045

regl

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
30510	0	16	0.995	8.6	5.125	1	2	5	9	12	14	15

lowest : 1 2 3 4 5 , highest: 12 13 14 15 16

 Value          1     2     3     4     5     6     7     8     9    10    11    12
 Frequency   1634  2213  1526  2150  1427  1192  2342  2191  2326  1277  1856  3241
 Proportion 0.054 0.073 0.050 0.070 0.047 0.039 0.077 0.072 0.076 0.042 0.061 0.106
                                   
 Value         13    14    15    16
 Frequency   1721  2571  1921   922
 Proportion 0.056 0.084 0.063 0.030

grpl

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
30510	0	48	0.999	25.3	16.11	2	5	14	26	38	44	46

lowest : 1 2 3 4 5 , highest: 44 45 46 47 48

grps

n	missing	distinct	Info	Mean	Gmd	.05	.10	.25	.50	.75	.90	.95
30510	0	121	1	61.56	40.21	6	12	32	62	91	110	115

lowest : 1 2 3 4 5 , highest: 117 118 119 120 121

tpa

n	missing	distinct	Info	Sum	Mean	Gmd
30510	0	2	0.672	10348	0.3392	0.4483

n	missing	distinct
30510	0	2

 Value         SK   tPA
 Frequency  20162 10348
 Proportion 0.661 0.339

Categorical variables

The nice thing of .html format is the possibility of using interactive plots. The plotly package allows you to render interactive plots. Simply place your cursor on top of the figure and all the information for a specific point will be shown.

p <- plot(d)
plotly::subplot(p[1])

Continuous variables

plotly::subplot(p[2])

Missings

There are no missings.

dd <- rms::datadist(df); options(datadist = "dd")
na.patterns <- Hmisc::naclus(df)
Hmisc::naplot(na.patterns, 'na per var')

Fractions of NAs per Variable.

Table 1

You can create a “Table1” directly in your .Rmd report, like done below.

df_table1 <- df %>% 
  select(
    tx,
    age,
    sex,
    Killip,
    pulse,
    sysbp,
    htn,
    dia,
    smk,
    pmi,
    ste,
    day30
    ) %>% 
  mutate(htn = ifelse(htn == 2, 1, 0))

tbl_gtsummary_custom <- 
  gtsummary::tbl_summary(
    df_table1,
    label = list(pulse ~ "Heart rate", 
                 sysbp ~ "Systolic Blood Pressure",
                 htn ~ "History of Hypertension",
                 dia ~ "Diabetes",
                 smk ~ "Smoking", 
                 pmi ~ "Previous MI",
                 ste ~ "Nbr ECG leads with ST-elevation",
                 day30 ~ "Dead in the first 30-days"), 
    by = tx, # split table by treatment received
    missing = "no" # don't list missing data separately
  ) %>%
  gtsummary::add_overall() %>% # add column with overall summary statistics
  gtsummary::add_n() %>% # add column with total number of non-missing observations
  gtsummary::modify_header(label = "**Variable**") # update the column header

#Add row headers
tbl_gtsummary_custom <- tbl_gtsummary_custom %>% 
  gtsummary::as_gt() %>% #convert to gt object and use gt functions
  gt::tab_row_group(label = "Outcome", rows = 20) %>% 
  gt::tab_row_group(label = "ECG findings", rows = 19) %>% 
  gt::tab_row_group(label = "CVRF, n (%)", rows = 12:18) %>% 
  gt::tab_row_group(label = "Vital signs", rows = 5:11) %>% 
  gt::tab_row_group(label = "Demographics", rows = 1:4) %>% 
  gt::tab_style(
    style = list(
      cell_fill(color = "#EFEFEF"),
      cell_text(weight = "bold")
    ),
    locations = cells_row_groups()
  )

tbl_gtsummary_custom

Variable	N	Overall, N = 30,510¹	SK, N = 20,162¹	tPA, N = 10,348¹
Demographics
age	30,510	62 (52, 70)	62 (52, 70)	62 (52, 70)
Sex	30,510
male		22,795 (75%)	15,070 (75%)	7,725 (75%)
female		7,715 (25%)	5,092 (25%)	2,623 (25%)
Vital signs
Killip Class	30,510
I		26,007 (85%)	17,209 (85%)	8,798 (85%)
II		3,857 (13%)	2,529 (13%)	1,328 (13%)
III		417 (1.4%)	275 (1.4%)	142 (1.4%)
IV		229 (0.8%)	149 (0.7%)	80 (0.8%)
Heart rate	30,510	73 (62, 86)	73 (62, 86)	73 (62, 86)
Systolic Blood Pressure	30,510	130 (112, 144)	130 (112, 144)	130 (112, 144)
CVRF, n (%)
History of Hypertension	30,510	11,635 (38%)	7,679 (38%)	3,956 (38%)
Diabetes	30,510	4,543 (15%)	3,040 (15%)	1,503 (15%)
Smoking	30,510
never		13,089 (43%)	8,654 (43%)	4,435 (43%)
quit		8,371 (27%)	5,542 (27%)	2,829 (27%)
current		9,050 (30%)	5,966 (30%)	3,084 (30%)
Previous MI	30,510	5,058 (17%)	3,320 (16%)	1,738 (17%)
ECG findings
Nbr ECG leads with ST-elevation	30,510	4 (3, 6)	4 (3, 6)	4 (3, 5)
Outcome
Dead in the first 30-days	30,510	2,128 (7.0%)	1,475 (7.3%)	653 (6.3%)
¹ Median (IQR); n (%)

However, you can also insert previously created html tables in your report. This is very handy because you do not need to write two times the same code. Usually you will have your full syntax code written in a .R syntax file and you will later create an .Rmd report for reporting main results, tables, plots, etc. If this is the case, you can save the table in html format from within your .R syntax file and insert it into your .Rmd file with the htmltools package.

rawHTML_Table1 <- paste(readLines(glue::glue("./Tables/Table1.html")), collapse = "\n")
htmltools::HTML(rawHTML_Table1)

Model

We are going to fit a logistic regression model. We want to obtain predicted probabilities with the model. Probabilities are obtained with the equation below.

\[ Probability = \frac{1}{1 + e^{(-(lp))}} \text{, where lp = } \alpha + x_1\beta_1 + x_2\beta_2 + x_n\beta_n \]

Yes, you can insert equations in R Markdown with LaTeX notation. Take a look at different LaTeX symbols.

options(prType = 'html') #set print type option to html. Default is 'plain'
model <- rms::lrm(day30 ~ rcs(age, 4)*sex + tx + Killip + rcs(pulse, 4) +
               rcs(sysbp, 4) + miloc + pmi, x = T, y = T, data = df)
print(model, digits = 4, table = TRUE, conf.int = 0.95, 
      coefs = TRUE, title = 'Logistic regression model')

Logistic regression model

 rms::lrm(formula = day30 ~ rcs(age, 4) * sex + tx + Killip + 
     rcs(pulse, 4) + rcs(sysbp, 4) + miloc + pmi, data = df, x = T, 
     y = T)

	Model Likelihood Ratio Test	Discrimination Indexes	Rank Discrim. Indexes
Obs 30510	LR χ² 3071.49	R² 0.241	C 0.820
0 28382	d.f. 20	g 1.319	D_xy 0.640
1 2128	Pr(>χ²) <0.0001	g_r 3.740	γ 0.641
max \|∂log L/∂β\| 2×10^-10		g_p 0.081	τ_a 0.083
		Brier 0.055

	β	S.E.	Wald Z	Pr(>\|Z\|)
Intercept	-1.0932	0.8338	-1.31	0.1898
age	0.0281	0.0147	1.91	0.0564
age'	0.0664	0.0326	2.03	0.0421
age''	-0.1643	0.1202	-1.37	0.1716
sex=female	-0.0077	1.7377	0.00	0.9965
tx=tPA	-0.2094	0.0530	-3.95	<0.0001
Killip=II	0.6094	0.0592	10.29	<0.0001
Killip=III	1.1516	0.1215	9.48	<0.0001
Killip=IV	1.8972	0.1635	11.60	<0.0001
pulse	-0.0070	0.0065	-1.08	0.2816
pulse'	0.0868	0.0234	3.71	0.0002
pulse''	-0.2355	0.0673	-3.50	0.0005
sysbp	-0.0409	0.0029	-14.34	<0.0001
sysbp'	0.0580	0.0099	5.86	<0.0001
sysbp''	-0.1467	0.0382	-3.84	0.0001
miloc=Other	0.2985	0.1352	2.21	0.0273
miloc=Anterior	0.5623	0.0516	10.90	<0.0001
pmi=yes	0.4850	0.0568	8.54	<0.0001
age × sex=female	-0.0017	0.0349	-0.05	0.9609
age' × sex=female	0.0654	0.0697	0.94	0.3481
age'' × sex=female	-0.3171	0.2404	-1.32	0.1871

Visualize Model

Suppose we would like to show different ways of visualizing/interpreting our model. We could show each Figure one below the other, but there is a more elegant way. Tabsets! Tabsets are very useful when wanting to report more than 1 Figure or Table.

Nomogram

plot(nomogram(model))

Nomogram.

Partial (conditional) effect plots

ggplot(rms::Predict(model, fun = plogis), rdata = df)

Partial (conditional) effect plots. Probability scale instead of default log odds scale.

sbp <- c(60, 80, 100, 120)
ggplot(rms::Predict(model, age, sysbp = sbp, fun = plogis))

and more

ggplot(rms::Predict(model, age, sysbp = sbp, Killip, fun = plogis))

Nested tabset

We can embedd one tabset in another.

heatmap

pred_intx <- rms::Predict(model, age, sysbp, Killip, fun = plogis, np = 100) 
col <- base::rev(grDevices::heat.colors(999, alpha = 0.8))
bounds <- rms::perimeter(df$age, df$sysbp, lowess. = T) #to see where data really exists

rms::bplot(
  pred_intx,
  perim = bounds,
  ylab = "sysbp",
  col.regions = col
  )

Heatmap showing predicted probabilities at different ages and systolic blood pressure for the 4 Killip classes.

Wireplot 3D

rms::bplot(
  pred_intx,
  lfun = wireframe,
  perim = bounds,
  ylab = "sysbp",
  zlab = "Pr(30-day Death)",
  shade = T
  )

3D plot

Conclusion

Hope this template will aid you when creating a .html report file with R Markdown. Note that since RStudio version version 1.4 or higher, R Markdown has incorporated a visual editing mode, making all aspects of creating and rendering a report very easy.

Computing Environment

sessioninfo::session_info(pkgs = c("attached"), include_base = T)

## ─ Session info ───────────────────────────────────────────────────────────────
##  setting  value
##  version  R version 4.1.2 (2021-11-01)
##  os       macOS Catalina 10.15.5
##  system   x86_64, darwin17.0
##  ui       X11
##  language (EN)
##  collate  en_US.UTF-8
##  ctype    en_US.UTF-8
##  tz       Europe/Zurich
##  date     2022-12-05
##  pandoc   2.18 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/tools/ (via rmarkdown)
## 
## ─ Packages ───────────────────────────────────────────────────────────────────
##  ! package      * version date (UTC) lib source
##    base         * 4.1.2   2021-11-01 [?] local
##    consort      * 1.0.1   2021-12-20 [1] CRAN (R 4.1.0)
##  P datasets     * 4.1.2   2021-11-01 [1] local
##    dplyr        * 1.0.9   2022-04-28 [1] CRAN (R 4.1.2)
##    Formula      * 1.2-4   2020-10-16 [1] CRAN (R 4.1.0)
##    ggplot2      * 3.3.5   2021-06-25 [1] CRAN (R 4.1.0)
##    glue         * 1.6.2   2022-02-24 [1] CRAN (R 4.1.2)
##  P graphics     * 4.1.2   2021-11-01 [1] local
##  P grDevices    * 4.1.2   2021-11-01 [1] local
##    gt           * 0.7.0   2022-08-25 [1] CRAN (R 4.1.2)
##    gtsummary    * 1.6.2   2022-09-30 [1] CRAN (R 4.1.2)
##    Hmisc        * 4.6-0   2021-10-07 [1] CRAN (R 4.1.0)
##    htmlwidgets  * 1.5.4   2021-09-08 [1] CRAN (R 4.1.0)
##    lattice      * 0.20-45 2021-09-22 [1] CRAN (R 4.1.2)
##  P methods      * 4.1.2   2021-11-01 [1] local
##    rms          * 6.2-0   2021-03-18 [1] CRAN (R 4.1.0)
##    SparseM      * 1.81    2021-02-18 [1] CRAN (R 4.1.0)
##  P stats        * 4.1.2   2021-11-01 [1] local
##    summarytools * 1.0.1   2022-05-20 [1] CRAN (R 4.1.2)
##    survival     * 3.4-0   2022-08-09 [1] CRAN (R 4.1.2)
##  P utils        * 4.1.2   2021-11-01 [1] local
## 
##  [1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library
## 
##  P ── Loaded and on-disk path mismatch.
## 
## ──────────────────────────────────────────────────────────────────────────────

Update History

You can create an update history section to show changes in your report over time.(e.g. someone asks for a new analysis, changes, etc).

Click to expand

Date	Changes
2022-12-05	Install Xquartz if willing to use the `summarytools` package
2022-12-04	Added example of how to insert references
2022-12-04	Added example of how to create a nested tabset
2022-12-03	Published

References

Allaire, JJ, Yihui Xie, Jonathan McPherson, Javier Luraschi, Kevin Ushey, Aron Atkins, Hadley Wickham, Joe Cheng, Winston Chang, and Richard Iannone. 2022. Rmarkdown: Dynamic Documents for r. https://CRAN.R-project.org/package=rmarkdown.

Xie, Yihui. 2022. Knitr: A General-Purpose Package for Dynamic Report Generation in r. https://yihui.org/knitr/.

Xie, Yihui, J. J. Allaire, and Garrett Grolemund. 2018. R Markdown: The Definitive Guide. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown.

Xie, Yihui, Christophe Dervieux, and Emily Riederer. 2020. R Markdown Cookbook. Boca Raton, Florida: Chapman; Hall/CRC. https://bookdown.org/yihui/rmarkdown-cookbook.

To learn prediction modelling the go-to source is Frank Harrell https://hbiostat.org/rmsc/ or Ewout Steyerberg https://link.springer.com/book/10.1007/978-0-387-77244-8 ↩︎

R Markdown Template

Pedro Lopez Ayala

05 December, 2022

Background

Data

Data dictionary

Data frame:df

Patient Flowchart

Descriptive statistics

Summary using `summarytools`

Summary using `Hmisc`

Categorical variables

Continuous variables

Missings

Table 1

Model

Visualize Model

Nomogram

Partial (conditional) effect plots

More

and more

Nested tabset

heatmap

Wireplot 3D

Conclusion

Computing Environment

Update History

References

R Markdown Template

Pedro Lopez Ayala

05 December, 2022

Background

Data

Data dictionary

Data frame:df

Patient Flowchart

Descriptive statistics

Summary using summarytools

Summary using Hmisc

Categorical variables

Continuous variables

Missings

Table 1

Model

Visualize Model

Nomogram

Partial (conditional) effect plots

More

and more

Nested tabset

heatmap

Wireplot 3D

Conclusion

Computing Environment

Update History

References

Summary using `summarytools`

Summary using `Hmisc`